Zinc in PDB 7y85: Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease Bound to Self Rna Target

The structure of Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease Bound to Self Rna Target also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease Bound to Self Rna Target (pdb code 7y85). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease Bound to Self Rna Target, PDB code: 7y85:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease Bound to Self Rna Target


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease Bound to Self Rna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:126.6 occ:1.00 ND1 A:HIS747 2.1 94.7 1.0 SG A:CYS752 2.3 81.5 1.0 SG A:CYS750 2.3 94.8 1.0 SG A:CYS755 2.3 83.8 1.0 CE1 A:HIS747 2.7 91.6 1.0 CB A:CYS755 3.1 68.9 1.0 CB A:CYS752 3.2 77.8 1.0 CG A:HIS747 3.3 91.7 1.0 CB A:CYS750 3.5 92.6 1.0 N A:CYS752 3.9 72.4 1.0 CB A:HIS747 3.9 91.3 1.0 N A:CYS755 4.0 70.9 1.0 NE2 A:HIS747 4.0 91.5 1.0 CA A:CYS752 4.1 72.6 1.0 CA A:CYS755 4.1 64.2 1.0 CD2 A:HIS747 4.3 92.3 1.0 CD A:LYS744 4.3 91.6 1.0 NZ A:LYS744 4.3 89.2 1.0 CA A:HIS747 4.5 90.4 1.0 C A:CYS750 4.5 93.8 1.0 CE A:LYS744 4.6 88.5 1.0 CA A:CYS750 4.6 94.1 1.0 O A:CYS750 4.7 96.0 1.0 C A:CYS752 4.8 79.8 1.0 N A:THR751 4.8 89.7 1.0 CE A:MET754 4.9 68.7 1.0

Zinc binding site 2 out of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease Bound to Self Rna Target


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease Bound to Self Rna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:126.2 occ:1.00 SG A:CYS491 2.3 96.9 1.0 SG A:CYS503 2.3 80.6 1.0 SG A:CYS501 2.3 81.1 1.0 SG A:CYS506 2.3 77.7 1.0 CB A:CYS506 2.9 55.3 1.0 CB A:CYS501 3.0 69.5 1.0 CB A:CYS491 3.3 78.8 1.0 CB A:CYS503 3.5 68.4 1.0 N A:CYS506 3.9 64.7 1.0 CA A:CYS506 4.0 35.0 1.0 O A:CYS501 4.2 67.8 1.0 CA A:CYS501 4.3 68.1 1.0 N A:CYS503 4.3 73.1 1.0 C A:CYS501 4.3 62.5 1.0 N A:CYS491 4.4 68.2 1.0 CA A:CYS491 4.4 70.4 1.0 CA A:CYS503 4.5 70.6 1.0 NH1 A:ARG480 4.5 52.9 1.0

Zinc binding site 3 out of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease Bound to Self Rna Target


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease Bound to Self Rna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1803 b:136.0 occ:1.00 SG A:CYS1414 2.3 92.4 1.0 SG A:CYS1018 2.3 92.8 1.0 SG A:CYS1417 2.3 95.3 1.0 SG A:CYS1406 2.3 87.5 1.0 CB A:CYS1417 2.9 77.2 1.0 CB A:CYS1018 3.4 88.2 1.0 CB A:CYS1414 3.5 80.5 1.0 CB A:CYS1406 3.6 90.3 1.0 N A:CYS1406 3.8 91.3 1.0 N A:CYS1414 4.0 78.3 1.0 CA A:CYS1417 4.1 69.9 1.0 N A:CYS1417 4.1 68.6 1.0 N A:CYS1018 4.2 87.2 1.0 CA A:CYS1406 4.3 91.7 1.0 CA A:CYS1414 4.3 81.7 1.0 CA A:CYS1018 4.3 87.6 1.0 NH2 A:ARG935 4.6 91.0 1.0 C A:PRO1405 4.8 89.5 1.0 C A:CYS1018 4.8 91.6 1.0 O A:CYS1018 4.8 96.8 1.0 CA A:PRO1405 4.9 87.1 1.0 CB A:ALA1020 4.9 86.3 1.0 O A:CYS1414 4.9 91.3 1.0 C A:CYS1414 5.0 83.3 1.0 NE A:ARG935 5.0 93.1 1.0

Zinc binding site 4 out of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease Bound to Self Rna Target


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna in Complex with Tpr-Chat Protease Bound to Self Rna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1805 b:118.6 occ:1.00 SG A:CYS130 2.3 71.0 1.0 SG A:CYS88 2.3 86.5 1.0 SG A:CYS127 2.3 80.8 1.0 SG A:CYS121 2.3 93.4 1.0 CB A:CYS121 3.1 92.9 1.0 CB A:CYS127 3.3 72.9 1.0 CB A:CYS130 3.3 64.5 1.0 CB A:CYS88 3.6 73.3 1.0 N A:CYS127 3.7 77.3 1.0 N A:CYS130 4.0 66.0 1.0 CA A:CYS127 4.0 72.5 1.0 N A:CYS88 4.1 77.2 1.0 CA A:CYS130 4.2 57.7 1.0 CA A:CYS88 4.4 76.2 1.0 CA A:CYS121 4.6 95.7 1.0 O A:CYS127 4.6 83.4 1.0 NH1 A:ARG135 4.6 69.4 1.0 C A:CYS127 4.6 75.7 1.0 C A:CYS88 4.8 77.3 1.0 C A:ALA126 4.8 80.4 1.0 N A:GLY90 4.8 64.1 1.0 ND2 A:ASN117 4.9 103.6 1.0 N A:CYS121 5.0 99.5 1.0 CA A:GLY90 5.0 62.0 1.0 CB A:PHE129 5.0 50.5 1.0

N.Cui, J.T.Zhang, Z.Li, X.Y.Liu, C.Wang, H.Huang, N.Jia. Structural Basis For the Non-Self Rna-Activated Protease Activity of the Type III-E Crispr Nuclease-Protease Craspase Nat Commun V. 13 7549 2022.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-022-35275-5